Starting the JR pass when you are still in Tokyo for a few days normally is a bad deal, use it for the days when you take the Shinkansen and travel substantial distances....
Exchanging the coupon at...

Exactly..... there's little reason to over-complicate things here regarding transportation, you only have 2 decent options with some minor variation for the last trek from the station if you use the...

I not only think it sucks but that it's incredibly stupid. The T&C's only mention calendar year, if you then implement a system that awards night credit based on check-out date you should be fired. ...